Re: [AMBER] Lone Pairs in AMBER FF

From: Carlos Simmerling <>
Date: Sat, 14 Mar 2020 11:18:40 -0400

Lone pairs are only modeled in a few force fields. Are you using one that
includes them?

On Sat, Mar 14, 2020, 10:35 AM 杨明俊 <> wrote:

> Hi All,
> I am trying to use AMBER18 to compute the hydration free energy of
> halogen substituted benzene with lone pairs. However, I can only get some
> information in section 17.7.4 of amber manual. In the manual, it says that
> the bonded terms are not computed with "frameon = 1" and only nonbonded
> (ele) terms will be computed.I have two questions to confirm in order to
> know how to prepare the input files (mol2 and frcmod) correctly:
> 1. how the position of the lone pair is determined from the input mol2 and
> frcmod files?
> 2. how does the lone pair evolve during MD simulations? Although in the
> manual it says "The lone pairs are kept in ideal geometry relative to local
> atoms, and resulting torques are transferred to these atoms", I still don't
> understand how it does in the code.
> Any of your information about getting better understanding of this
> question is appreciated!
> Thanks in advance!
> Mingjun
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Received on Sat Mar 14 2020 - 08:30:02 PDT
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